Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes.
Inability of Prevotella bryantii to form a functional Shine-Dalgarno interaction reflects unique evolution of ribosome binding sites in Bacteroidetes.
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DOI：
10.1371/journal.pone.0022914
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Avguštin G
中科院分区：
文献类型：
--
作者：
Accetto T;Avguštin G
Shine-Dalgarno（SD）序列是指导翻译起始于真实起始密码子的关键元件，也使翻译起始能够在含有中等强度二级结构的5′非翻译mRNA区域（5′-UTR）中进行。然而，对来自主要细菌门拟杆菌门的近40个基因组的生物信息学分析显示，SD序列普遍缺失，GC含量下降，因此在5′-UTR中形成二级结构的趋势降低。利用布氏普雷沃氏菌TC 1 -1表达系统进行的实验与这些发现一致：在非结构化5′-UTR中添加或缺失SD序列均不影响报告蛋白、非特异性核酸酶NucB的水平。此外，与大肠杆菌中的hMGFP水平相反，当SD序列形成具有约5.2 kcal/mol折叠能的二级结构的一部分时，布氏毕赤酵母TC 1 -1中的NucB水平低五倍。此外，延长的SD序列不影响蛋白质水平，如在E。杆菌因此，尽管反SD序列存在于其基因组的16 S rRNA基因中，但在布氏毕赤酵母TC 1 -1和可能的拟杆菌门的其他成员中，在翻译起始期间似乎不发生功能性SD相互作用。因此，我们认为，在不存在SD序列相互作用的情况下，拟杆菌中真正的起始密码子的选择是通过核糖体蛋白S1与非结构化的5′-UTR结合来完成的，而不是由于mRNA二级结构而无法接近的编码区。此外，我们发现起始密码子前区域的序列标志可以用作分类标记。根据是否使用完整的序列标识或仅使用其一部分，如特定位置的信息含量和碱基比例，可以区分细菌属或科，在某些情况下甚至细菌门。
The Shine-Dalgarno (SD) sequence is a key element directing the translation to initiate at the authentic start codons and also enabling translation initiation to proceed in 5′ untranslated mRNA regions (5′-UTRs) containing moderately strong secondary structures. Bioinformatic analysis of almost forty genomes from the major bacterial phylum Bacteroidetes revealed, however, a general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5′-UTRs. The experiments using the Prevotella bryantii TC1-1 expression system were in agreement with these findings: neither addition nor omission of SD sequence in the unstructured 5′-UTR affected the level of the reporter protein, non-specific nuclease NucB. Further, NucB level in P. bryantii TC1-1, contrary to hMGFP level in Escherichia coli, was five times lower when SD sequence formed part of the secondary structure with a folding energy -5,2 kcal/mol. Also, the extended SD sequences did not affect protein levels as in E. coli. It seems therefore that a functional SD interaction does not take place during the translation initiation in P. bryanttii TC1-1 and possibly other members of phylum Bacteroidetes although the anti SD sequence is present in 16S rRNA genes of their genomes. We thus propose that in the absence of the SD sequence interaction, the selection of genuine start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5′-UTR as opposed to coding region which is inaccessible due to mRNA secondary structure. Additionally, we found that sequence logos of region preceding the start codons may be used as taxonomical markers. Depending on whether complete sequence logo or only part of it, such as information content and base proportion at specific positions, is used, bacterial genera or families and in some cases even bacterial phyla can be distinguished.
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影响因子：
3.2
作者：
Miyazaki, K;Miyamoto, H;Flint, HJ
通讯作者：
Flint, HJ
影响因子：
5.6
作者：
DESMIT, MH;VANDUIN, J
通讯作者：
VANDUIN, J
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.
DOI：
10.1073/pnas.1002036107
发表时间：
2010-04-06
影响因子：
11.1
作者：
Nakagawa, So;Niimura, Yoshihito;Gojobori, Takashi
通讯作者：
Gojobori, Takashi
DOI：
10.1111/j.1365-2672.1995.tb03156.x
发表时间：
1995-10-01
期刊：
JOURNAL OF APPLIED BACTERIOLOGY
影响因子：
--
作者：
DANIEL, AS;MARTIN, J;FLINT, HJ
通讯作者：
FLINT, HJ